Recent changes to pubsearch-bugs

can't add new hits to a publication

kate — Tue, 29 Jan 2008 08:43:28 -0000

When I try to add new hits from my laptop in the context of the PubSearch "Article/Display Update page, I first click on "Add new hits", nothing happens when I type in a gene name and then click "Search."

display entered_by/date info on Phenotype detail page

Tanya Berardini — Fri, 15 Dec 2006 19:35:57 -0000

Related Germplasms section:

In addition to the existing info on updated_by/date, please add another column with entered_by/date.

Thanks.

alias display on hit detail pages

Tanya Berardini — Tue, 24 Oct 2006 21:15:03 -0000

please separate aliases of genes using a pipe (|),
instead of a space. It is hard to tell when one alias
ends and another begins.

fix germplasm search

Christophe Tissier — Thu, 28 Sep 2006 20:47:14 -0000

The germplasm search is currently set as an 'exact'
search although it should be a 'contains' search....
which probably explains why I can never find anything :)

Thanks for fixing that.

Chris

EASY:adjust display of entries on dropdown

Tanya Berardini — Thu, 14 Sep 2006 18:21:49 -0000

of Mutation Site on Allele Detail page. For example:

http://tesuque.stanford.edu:8080/pub/Display?acc=allele:170184

Allele Mode
Mutation Site
Mutagen

The one in the position above should only be "genic"
and "intergenic region". Remove all other choices.

Add Affinity Chromatography to the description of IPI

donghui — Wed, 30 Aug 2006 00:17:35 -0000

I propose we add 'affinity chromatography' into the
[description] column of evidence type IPI.

I have come across several examples which could not
fall into any of the existing descriptions. Currently
we have the following types of description in PubSearch
for IPI:

CO-IP
CO-purification
CO-sedimentation
Far-western
FRET
Fusion protein pull down
SOS-recruitment
split ubiquitin
yeast one hybrid
yeast two hybrid

Thanks for your comments.

Donghui

Simplify the PubSearch [Add Allele] pages

donghui — Fri, 25 Aug 2006 00:11:57 -0000

PubSearch [Add Allele]

I found the [add allele] function in the current
version of PubSearch is confusing and can be simplified:

When I click [add allele] under the [Allele
Associations] section, I will be prompted to a page
[Add Allele]. After all the information is added, I
click [update]. This will lead to a new page. On
this page, the top half is virtually exact the same as
previous [Add Allele] page. I wonder if we could
combine these two pages together, so that we could type
in all the relevant information on the same page.

I'll be happy to do a demonstration.

Donghui

two different base URLs generated for article link

Tanya Berardini — Mon, 21 Aug 2006 17:03:45 -0000

http://tesuque.stanford.edu:8080/pub/pdfs/12345.pdf
(1615 articles with this link format)
and
http://tesuque.stanford.edu/pubsearch/documents/56789.pdf
(11939 articles with this link format)

Don't know why there are two different ones. The
latter does not work if plugged into a browser. I
looked around a bit and found some code that might be
pertinent in:

when in pubsearch directory:

/WEB-INF/classes/pub/beans/ArticleBeanImpl.java

(getPdflink, I believe)

cannot select terms that contain apostrophe

Christophe Tissier — Wed, 16 Aug 2006 17:55:33 -0000

terms containing an apostrophe cannot be used to
annotate genes, irrespective of whether the term is
temporary or not.
Currently, one needs to remove the apostrophe, save,
chose the term, and reinstate the apostrophe once the
term is chosen... pretty time consuming.

Thanks for looking into it.

Chris

for a more specific example try to use (+)-abscisic
acid 8'-hydroxylase activity

add pub_article.is_scanned info to several pages

Tanya Berardini — Tue, 01 Aug 2006 21:57:37 -0000

Can we display a paper's is_scanned status on the
following pages (in order of importance):

1. Hit result page

2. GO annotation page

For example:
http://tesuque.stanford.edu:8080/pub/DisplayAnnotation?term_id=84873

3. Gene reference list page

For example:

http://tesuque.stanford.edu:8080/pub/jsp/display/ReferenceList.jsp?acc=term:84873

4. Locus reference list page

For example:

http://tesuque.stanford.edu:8080/pub/jsp/display/ReferenceList.jsp?acc=locus:20053